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Tag pdb [65 articles]

Recent papers classified by the tag pdb.
  • Transmembrane proteins in the Protein Data Bank: identification and classification.
    Bioinformatics, Vol. 20, No. 17. (22 November 2004), pp. 2964-2972.
    by GE Tusnády, Z Dosztányi, I Simon
    posted to pdb membrane_protein by viktor21614 on 2008-07-22 15:33:11 as ** along with 3 people and 1 group chrn xdeupi sebk LabCompMed
  • The Protein Data Bank.
    Nucleic Acids Res, Vol. 28, No. 1. (1 January 2000), pp. 235-242.
    by HM Berman, J Westbrook, Z Feng, G Gilliland, TN Bhat, H Weissig, IN Shindyalov, PE Bourne
    posted to database pdb by vavi on 2006-07-17 09:09:40 as ** along with 22 people and 4 groups sebk higueruelo boris_aguilar nigham lillekatt thaliana dimka kuhn jwm bicko itmeson dgront caporaso condon leelarcombe aengisch debatebob massivemayhem gisle girschick selrac tji Radiation_Damage Stressosome biomedical-nlp beta
  • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential.
    Fold Des, Vol. 2, No. 3. (1997), pp. 173-181.
    by I Bahar, AR Atilgan, B Erman
    posted to pdb by simone on 2006-02-23 16:28:32 as ** along with 3 people apaydin lna aqeel
  • Large macromolecular complexes in the Protein Data Bank: a status report.
    Structure (Camb), Vol. 13, No. 3. (March 2005), pp. 381-388.
    by S Dutta, HM Berman
    posted to pdb by simone on 2005-08-10 12:41:37 as read
  • The Protein Data Bank.
    Acta Crystallogr D Biol Crystallogr, Vol. 58, No. Pt 6 No 1. (June 2002), pp. 899-907.
    by HM Berman, T Battistuz, TN Bhat, WF Bluhm, PE Bourne, K Burkhardt, Z Feng, GL Gilliland, L Iype, S Jain, P Fagan, J Marvin, D Padilla, V Ravichandran, B Schneider, N Thanki, H Weissig, JD Westbrook, C Zardecki
    posted to database pdb protein structure by siebertm on 2007-04-25 12:40:29 as *
  • Mapping PDB chains to UniProtKB entries.
    Bioinformatics, Vol. 21, No. 23. (1 December 2005), pp. 4297-4301.
    by AC Martin
    posted to uniprot pdb mapping by saunders on 2008-07-24 10:51:12 as *** along with 3 people bicko grahamc lpfernandes
  • Cotranslational protein folding--fact or fiction?
    Bioinformatics, Vol. 23, No. 13. (1 July 2007)
    by CM Deane, M Dong, FP Huard, BK Lance, GR Wood
    posted to co-translation folding pdb protein by saunders on 2007-11-22 17:01:37 as read along with 2 people cdeane Pao-Yang
  • A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships.
    J Chem Inf Model, Vol. 46, No. 2. (r 2006), pp. 736-742.
    by ND Gold, RM Jackson
    posted to sites pdb hashing geometric binding by reyez on 2008-07-16 09:29:52 as ** along with 3 people and 1 group massivemayhem caporaso blackbart biomedical-nlp
  • Announcing the worldwide Protein Data Bank
    Nat Struct Mol Biol, Vol. 10, No. 12. (December 2003), pp. 980-980.
    by Helen Berman, Kim Henrick, Haruki Nakamura
    posted to wwpdb pdb by reyez on 2008-07-18 10:27:12 as ** along with 2 people allmensch massivemayhem
  • Realism about PDB
    Nature Biotechnology, Vol. 25, No. 8., pp. 845-846.
    by Helen M Berman, Kim Henrick, Haruki Nakamura, John Markley, Philip E Bourne, John Westbrook
    posted to wwpdb pdb by reyez on 2008-07-18 10:26:42 as ** along with 1 person hpiwowar
  • The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.
    Nucleic acids research, Vol. 35, No. Database issue. (January 2007)
    by H Berman, K Henrick, H Nakamura, JL Markley
    posted to wwpdb pdb by reyez on 2008-07-18 10:27:18 as **
  • Janocchio - a Java applet for viewing 3D structures and calculating NMR couplings and NOEs
    Magnetic Resonance in Chemistry, Vol. 45, No. 7. (2007), pp. 595-600.
    by David A Evans, Michael J Bodkin, Richard S Baker, Gary J Sharman
    posted to nmr pdb structure visualization by paridep on 2007-07-25 17:41:52 as read along with 2 people daevans egonw
  • Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor.
    Structure, Vol. 5, No. 8. (15 August 1997), pp. 997-1015.
    by FA Quiocho, JC Spurlino, LE Rodseth
    posted to 3mbp maltose pdb by nigham on 2008-01-15 08:46:54 as * along with 1 person papatonyhill
  • Structural basis of light harvesting by carotenoids: peridinin-chlorophyll-protein from Amphidinium carterae.
    Science (New York, N.Y.), Vol. 272, No. 5269. (21 June 1996), pp. 1788-1791.
    by E Hofmann, PM Wrench, FP Sharples, RG Hiller, W Welte, K Diederichs
    posted to thesis pdb 1ppr by nigham on 2008-06-30 05:13:23 as **
  • Effect of cavity-creating mutations in the hydrophobic core of chymotrypsin inhibitor 2.
    Biochemistry, Vol. 32, No. 42. (26 October 1993), pp. 11259-11269.
    by SE Jackson, M Moracci, N elMasry, CM Johnson, AR Fersht
    posted to thesis pdb 1coa by nigham on 2008-07-17 07:09:55 as **
  • Optimization of P1-P3 groups in symmetric and asymmetric HIV-1 protease inhibitors.
    European journal of biochemistry / FEBS, Vol. 270, No. 8. (April 2003), pp. 1746-1758.
    by HO Andersson, K Fridborg, S Löwgren, M Alterman, A Mühlman, M Björsne, N Garg, I Kvarnström, W Schaal, B Classon, A Karlén, UH Danielsson, G Ahlsén, U Nillroth, L Vrang, B Oberg, B Samuelsson, A Hallberg, T Unge
    posted to thesis pdb 1ebz by nigham on 2008-06-29 09:57:47 as **
  • The atomic resolution crystal structure of atratoxin determined by single wavelength anomalous diffraction phasing.
    The Journal of biological chemistry, Vol. 279, No. 37. (10 September 2004), pp. 39094-39104.
    by X Lou, Q Liu, X Tu, J Wang, M Teng, L Niu, DJ Schuller, Q Huang, Q Hao
    posted to thesis pdb 1v6p by nigham on 2008-06-30 05:16:08 as **
  • Structure of an E6AP-UbcH7 Complex: Insights into Ubiquitination by the E2-E3 Enzyme Cascade
    Science, Vol. 286, No. 5443. (12 November 1999), pp. 1321-1326.
    by Lan Huang, Elspeth Kinnucan, Guangli Wang, Sylvie Beaudenon, Peter M Howley, Jon M Huibregtse, Nikola P Pavletich
    posted to pdb ubiquitin by nigham on 2008-01-15 09:02:49 as *
  • Conformational Flexibility Underlies Ubiquitin Ligation Mediated by the WWP1 HECT Domain E3 Ligase
    Molecular Cell, Vol. 11, No. 1. (January 2003), pp. 249-259.
    by Mark A Verdecia, Claudio A Joazeiro, Nicholas J Wells, Jean-Luc Ferrer, Marianne E Bowman, Tony Hunter, Joseph P Noel
    posted to pdb ubiquitin by nigham on 2008-01-15 08:59:40 as *
  • Detection and characterization of xenon-binding sites in proteins by 129Xe NMR spectroscopy.
    J Mol Biol, Vol. 322, No. 2. (13 September 2002), pp. 425-440.
    by SM Rubin, SY Lee, EJ Ruiz, A Pines, DE Wemmer
    posted to 1lls maltose pdb by nigham on 2008-02-14 02:15:30 as *
  • Sugar-binding and crystallographic studies of an arabinose-binding protein mutant (Met108Leu) that exhibits enhanced affinity and altered specificity.
    Biochemistry, Vol. 30, No. 28. (16 July 1991), pp. 6861-6866.
    by PS Vermersch, DD Lemon, JJ Tesmer, FA Quiocho
    posted to pdb by nigham on 2008-02-14 01:59:13 as * along with 1 person papatonyhill
  • Involvement of the C terminus in intramolecular nitrogen channeling in glucosamine 6-phosphate synthase: evidence from a 1.6 A crystal structure of the isomerase domain.
    Structure, Vol. 6, No. 8. (15 August 1998), pp. 1047-1055.
    by A Teplyakov, G Obmolova, MA Badet-Denisot, B Badet, I Polikarpov
    posted to pdb by nigham on 2008-02-14 01:57:31 as *
  • The CATH database: an extended protein family resource for structural and functional genomics
    Nucl. Acids Res., Vol. 31, No. 1. (1 January 2003), pp. 452-455.
    by FMG Pearl, CF Bennett, JE Bray, AP Harrison, N Martin, A Shepherd, I Sillitoe, J Thornton, CA Orengo
    posted to structural pdb families cath by nigham on 2008-07-02 13:34:59 as **
  • Crystal structure of thiaminase-I from Bacillus thiaminolyticus at 2.0 A resolution.
    Biochemistry, Vol. 37, No. 45. (10 November 1998), pp. 15981-15989.
    by N Campobasso, CA Costello, C Kinsland, TP Begley, SE Ealick
    posted to thesis pdb 2thi by nigham on 2008-07-02 12:59:11 as *
  • Protein intermediate trapped by the simultaneous crystallization process. Crystal structure of an iron-saturated intermediate in the Fe3+ binding pathway of camel lactoferrin at 2.7 a resolution.
    The Journal of biological chemistry, Vol. 276, No. 39. (28 September 2001), pp. 36817-36823.
    by JA Khan, P Kumar, A Srinivasan, TP Singh
    posted to thesis pdb 1i6q by nigham on 2008-07-02 12:57:16 as **
  • Structure of human apolactoferrin at 2.0 A resolution. Refinement and analysis of ligand-induced conformational change.
    Acta crystallographica. Section D, Biological crystallography, Vol. 54, No. Pt 6 Pt 2. (1 November 1998), pp. 1319-1335.
    by GB Jameson, BF Anderson, GE Norris, DH Thomas, EN Baker
    posted to thesis pdb 1cb6 by nigham on 2008-07-02 12:54:57 as **
  • Molecular replacement solution of the structure of apolactoferrin, a protein displaying large-scale conformational change.
    Acta crystallographica. Section B, Structural science, Vol. 47 ( Pt 6) (1 December 1991), pp. 998-1004.
    by GE Norris, BF Anderson, EN Baker
    posted to thesis pdb by nigham on 2008-07-02 11:25:32 as *
  • Solution structure of the PX domain, a target of the SH3 domain.
    Nat Struct Biol, Vol. 8, No. 6. (June 2001), pp. 526-530.
    by H Hiroaki, T Ago, T Ito, H Sumimoto, D Kohda
    posted to 1gd5 pdb by nigham on 2008-02-14 04:21:18 as ** along with 1 person kallberg
  • Solution structure of the Vam7p PX domain.
    Biochemistry, Vol. 41, No. 19. (14 May 2002), pp. 5956-5962.
    by J Lu, J Garcia, I Dulubova, TC Südhof, J Rizo
    posted to 1kmd pdb by nigham on 2008-02-14 04:19:29 as *
  • TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.
    Protein Sci, Vol. 6, No. 11. (November 1997), pp. 2308-2323.
    by AC Wallace, N Borkakoti, JM Thornton
    posted to algorithm application geometric-hashing pdb structure-searching by nickolay on 2005-12-09 20:34:22 as *** along with 3 people shadowman tjimenez jwm
  • Three-dimensional profiles: a new tool to identify protein surface similarities.
    J Mol Biol, Vol. 284, No. 4. (11 December 1998), pp. 1211-1221.
    by M de Rinaldis, G Ausiello, G Cesareni, M Helmer-Citterich
    posted to algorithm application msa pattern pdb structure-searching surface by nickolay on 2005-12-08 23:39:24 as ** along with 1 person dgront
  • Recovering the true targets of specific ligands by virtual screening of the protein data bank.
    Proteins, Vol. 54, No. 4. (1 March 2004), pp. 671-680.
    by N Paul, E Kellenberger, G Bret, P Müller, D Rognan
    posted to docking pdb protein-ligand virtual-screening by nickolay on 2005-12-06 02:12:24 as ** along with 2 people BragilMassoud insilico
  • Supersites within superfolds. Binding site similarity in the absence of homology
    Journal of Molecular Biology, Vol. 282, No. 4. (2 October 1998), pp. 903-918.
    by Robert B Russell, Peter D Sasieni, Michael J Sternberg
    posted to alignment binding domain-classification pdb protein-ligand structure-activity by nickolay on 2005-12-08 23:16:10 as **** along with 1 person chad_davis
  • Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions.
    J Mol Biol, Vol. 326, No. 2. (14 February 2003), pp. 607-620.
    by M Hendlich, A Bergner, J Günther, G Klebe
    posted to application binding database moad pdb protein-ligand by nickolay on 2005-12-06 02:10:41 as read along with 2 people blackbart massivemayhem
  • PostDOCK: a structural, empirical approach to scoring protein ligand complexes.
    J Med Chem, Vol. 48, No. 22. (3 November 2005), pp. 6821-6831.
    by C Springer, H Adalsteinsson, MM Young, PW Kegelmeyer, DC Roe
    posted to application docking machine-learning pdb protein-ligand surface by nickolay on 2005-12-06 01:52:55 as **** along with 1 person and 2 groups sangeetha Bioinformatics insilicodrug
  • Structural characterization of proteins using residue environments.
    Proteins, Vol. 61, No. 4. (1 December 2005), pp. 741-747.
    by SD Mooney, MH Liang, R DeConde, RB Altman
    posted to algorithm domain-classification pdb side-chains structure-classification by nickolay on 2005-12-16 16:29:55 as *** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Andrew Bordner, Andrey Gorin
    posted to complex protein-protein pdb interface interaction bioinformatics by neils on 2008-05-13 00:10:20 as ** along with 1 person phoenixzxl
  • The protein structure prediction problem could be solved using the current PDB library.
    Proc Natl Acad Sci U S A, Vol. 102, No. 4. (25 January 2005), pp. 1029-1034.
    by Y Zhang, J Skolnick
    posted to structure protein prediction pdb modelling homology casp by neils on 2008-06-12 07:42:10 as ** along with 9 people and 3 groups karbak iakes vavi marcius alexg j3xucite kracher schuylrp jfmuggs BioinfoCIPF Immunoinformatics SGU-CIPF
  • Structure of the catalytic domain of fibroblast collagenase complexed with an inhibitor.
    Science (New York, N.Y.), Vol. 263, No. 5145. (21 January 1994), pp. 375-377.
    by B Lovejoy, A Cleasby, AM Hassell, K Longley, MA Luther, D Weigl, G McGeehan, AB McElroy, D Drewry, MH Lambert
    posted to pdb drug-discovery by massivemayhem on 2008-07-01 14:02:40 as **
  • Quantitative analysis of nucleic acid three-dimensional structures.
    J Mol Biol, Vol. 308, No. 5. (18 May 2001), pp. 919-936.
    by P Gendron, S Lemieux, F Major
    posted to pdb rna structure by marcius on 2005-12-20 07:08:31 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • The structure of melittin in the form I crystals and its implication for melittin's lytic and surface activities.
    Biophys. J., Vol. 37, No. 1. (1 January 1982), pp. 353-361.
    by TC Terwilliger, L Weissman, D Eisenberg
    posted to melittin pdb by loison on 2008-03-27 09:01:29 as **
  • The structure of melittin. I. Structure determination and partial refinement
    J. Biol. Chem., Vol. 257, No. 11. (10 June 1982), pp. 6010-6015.
    by TC Terwilliger, D Eisenberg
    posted to melittin pdb by loison on 2008-03-27 08:58:07 as **
  • Crystal structure of the collagen triple helix model [(Pro-Pro-Gly)10]3
    Protein Sci, Vol. 11, No. 2. (1 February 2002), pp. 262-270.
    by Rita Berisio, Luigi Vitagliano, Lelio Mazzarella, Adriana Zagari
    posted to collagen pdb structure by loison on 2008-03-20 12:55:30 as **
  • Efflux-mediated antiseptic resistance gene qacA from Staphylococcus aureus: common ancestry with tetracycline- and sugar-transport proteins.
    Mol Microbiol, Vol. 4, No. 12. (December 1990), pp. 2051-2062.
    by DA Rouch, DS Cram, D DiBerardino, TG Littlejohn, RA Skurray
    posted to crystalviolet experiments pdb protein structure by loison on 2006-09-29 22:27:45 as **
  • Structural mechanism of the simultaneous binding of two drugs to a multidrug-binding protein.
    EMBO J, Vol. 23, No. 15. (4 August 2004), pp. 2923-2930.
    by MA Schumacher, MC Miller, RG Brennan
    posted to experiment pdb protein qacr by loison on 2006-10-09 10:36:38 as **
  • Crystal structures of QacR-diamidine complexes reveal additional multidrug-binding modes and a novel mechanism of drug charge neutralization.
    J Biol Chem, Vol. 279, No. 14. (2 April 2004), pp. 14365-14371.
    by DS Murray, MA Schumacher, RG Brennan
    posted to experiment pdb protein qacr by loison on 2006-10-09 10:31:57 as ***
  • The relationship between the sequence identities of alpha helical proteins in the PDB and the molecular similarities of their ligands.
    J Chem Inf Comput Sci, Vol. 41, No. 6. (c 2001), pp. 1617-1622.
    by JB Mitchell
    posted to chemical pdb protein similarity structure by kuhn on 2007-06-06 13:44:13 as **
  • SuperLigands - a database of ligand structures derived from the Protein Data Bank.
    BMC Bioinformatics, Vol. 6, No. 1. (19 May 2005)
    by E Michalsky, M Dunkel, A Goede, R Preissner
    posted to chemical database pdb similarity by kuhn on 2005-12-19 14:38:44 as ** along with 1 person ucbcjbm
  • Intrinsic disorder in the Protein Data Bank.
    Journal of biomolecular structure & dynamics, Vol. 24, No. 4. (February 2007), pp. 325-342.
    by T Le Gall, PR Romero, MS Cortese, VN Uversky, AK Dunker
    posted to disorder iup pdb protein by kluck on 2008-04-17 08:55:45 as ***
  • PDBcal: A Comprehensive Dataset for Receptor-Ligand Interactions with Three-dimensional Structures and Binding Thermodynamics from Isothermal Titration Calorimetry
    Chemical Biology & Drug Design, Vol. 71, No. 6. (2008), pp. 529-532.
    by Liwei Li, Justin J Dantzer, Jonathan Nowacki, Brian J O’callaghan, Samy O Meroueh
    posted to thermo sm-prot pdb 2008 by higueruelo on 2008-05-26 19:55:04 as ** along with 2 people kintoki massivemayhem
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